[Bioperl-l] Raw data chromatograms

[Malay]

fabrizio at cribi.unipd.it wrote:
> Hi! 
>  
> I'm a new user of bioperl! 
> I'm trying to make a script in order to identify contaminations between two 
> sequences analyzed by capillary neighbors in the 3730XL DNA Sequencer. 
> "Manually" this fact can be seen by looking at the chromatograms of 
> the raw data (for example in program "sequence analysis" of Applied 
> Biosystems). 
> The simplest thing is probably to study the correlation coefficient in a 
> certain time window; however, in order to do that I must get the trace of 
> the different bases from the ABI files. 
> The ABI.pm module seems to me only to detect the traces that make up the 
> final chromatogram, in which it is nearly impossible to see possibile 
> contaminations (as the peaks have already been analyzed and modified). 

I am not very sure what you mean by "analyzed and modified". The 
basecalls tracks given by the "ABI.pm" is separate from the raw trace 
value returned. The traces returned by the ABI.pm are indeed the raw 
traces. To draw the cromatogram, there are two more step you need to do. 
Normalize each trace value by diving with the largest trace value, and 
recognize the peaks from the base-calling track.

Ofcourse any discussion on ABI.pm is beyond the scope of Bioperl mailing 
list. ABI.pm is not a module in BioPerl distribution. Please write to me 
separately if you have any other question regarding ABI.pm.

Malay